tbuckley/cabot-search huggingface dataset:
Abstract 255: Isolation of unaltered sub-populations of immune cells using magnetic levitation
Authors: Kevin Travers, Nathan Wilson, Abhijit Kale
Journal: Cancer Research (2023)

Abstract The analysis and characterization of subsets of immune cells from heterogeneous samples, such as peripheral blood mononuclear cells (PBMCs), requires isolation and enrichment. Common methods for this enrichment step include fluorescence activated cell sorting and positive or negative selection with magnetic beads. However, these methods alter native cell phenotypes during the enrichment process by the application of pressure, binding of antibodies, extensive manipulation and centrifugation, among other perturbations. This results in altered gene expression, generating molecular profiles that are not representative of true biological significance. These alterations are prevented by using magnetic levitation cell isolation and enrichment. The LeviCellTM platform performs hands-free cell enrichment by utilizing magnetic fields to levitate viable, healthy cells away from dead cells and debris. Unlike other single cell separation methods, the enriched target cells are not subject to mechanical force, labeling, or staining to achieve viability enrichment. This results in a single cell suspension that is ready for immediate downstream analysis, producing molecular profiles free of isolation-induced gene expression artifacts. We have developed reagents to extend the benefits of this technology to the immuno-oncology research market. These new reagents are used to target the enrichment of all T cells, the CD4+ or CD8+ subsets of T cells, or all B cells, with other target populations in development. In all cases, unwanted cells are captured within the levitation chamber, depleting them from the sample. These reagents leverage the magnetic field across the levitation chamber. Specifically-tagged, unwanted cells are pulled to the edges of the levitation chamber while the target cells undergo viable cell enrichment. The end result is a cell population that has been enriched and at higher viability. We have seen consistent depletion rates of &amp;gt;98%, resulting in a final targeted population with 90% or higher purity in most cases. Here we demonstrate the performance of the LeviCell platform in the enrichment of targeted cell populations relevant to the immuno-oncology research community. Citation Format: Kevin Travers, Nathan Wilson, Abhijit Kale. Isolation of unaltered sub-populations of immune cells using magnetic levitation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 255.
Abstract 5896: Identification of microbial biomarkers to predict recurrence of oral squamous cell carcinoma
Authors: Wei-Ni Lyu, Mei-Chun Lin, Pei-Jen Lou, Liang-Chuan Lai, Mong-Hsun Tsai
Journal: Cancer Research (2023)

Abstract Introduction: Oral cancer is a fatal cancer and the sixth most common neoplasm worldwide. Over 90% of oral cancer is oral squamous cell carcinoma (OSCC). OSCC is a global health problem because of its late diagnosis and high rate of relapse and metastasis. Currently, cumulative evidence has suggested the association between oral microbiome and oral cancer. However, the correlation between the oral microbiome and OSCC recurrence remained unclear. Therefore, we investigated the OSCC patients’ oral microbiota to understand the roles of oral microbiome in the recurrence of OSCC. Materials and Methods: To evaluate the role of the oral microbiome in the recurrence of oral cancer, we compared the oral bacterial composition of tumor samples from the OSCC patients with or without recurrence based on 16S rRNA amplicon sequencing of 54 oral swab samples. Then, the structures of the oral microbiome were analyzed to establish a prediction model for the recurrence of OSCC. To identify microbial signatures capable of distinguishing recurrence from non-recurrence, the 54 tumor samples from OSCC patients were used as a training dataset. Furthermore, 46 external tumor samples from other OSCC patients were used to validate the dataset. Results: The oral bacterial compositions differed in OSCC patients between with and without recurrence. Compared to nonrecurrence OSCC, periodontitis-related bacteria were enriched in OSCC recurrence. Functional analysis of the oral microbiome showed several functions associated with OSCC recurrence including amino acid metabolism, carbohydrate metabolism, lipid metabolism, glucose utilization, and drug resistance. Subsequently, we established a random forest prediction model with high accuracy (accuracy = 0.963) to discriminate OSCC recurrence from the original OSCC based on five specific microbial signatures. Moreover, the prediction model achieved an accuracy of 0.761 in another independent cohort (46 OSCC patients). On the other hand, the accuracy predicted by the current clinical-used model was 0.519 with the training dataset. Thus, our novel model could improve the prediction accuracy of OSCC recurrence. Conclusions: In this study, we elucidated the relationship between oral bacteria and the recurrence of OSCC. Moreover, we established a novel bacteria-based prediction model for the recurrence of OSCC. Thus, the present study provided a new insight and treatment strategy for the clinical prediction of OSCC recurrence. Citation Format: Wei-Ni Lyu, Mei-Chun Lin, Pei-Jen Lou, Liang-Chuan Lai, Mong-Hsun Tsai. Identification of microbial biomarkers to predict recurrence of oral squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5896.
Abstract 6142: Inhibition of both MAPK and AKT pathways overcomes resistance of NRAS-mutant melanoma stem cells to apoptosis
Authors: Ryyan Alobaidi, Nusrat Islam, Yanjun R. Zhang, Mathew M. Shamo, Samuel Allsup, Cynthia M. Simbulan-Rosenthal, Dean S. Rosenthal
Journal: Cancer Research (2023)

Abstract Malignant melanoma is a lethal skin cancer containing melanoma-initiating cells (MIC) implicated in tumorigenesis, invasion, and drug resistance, and characterized by elevated expression of stem cell markers, such as CD133. We have shown that siRNA knockdown of CD133 enhanced apoptosis induced by the MEK inhibitor trametinib in melanoma cells. The current study investigates the underlying mechanisms of CD133's anti-apoptotic activity in patient-derived BAKP melanoma, harboring the difficult-to-treat NRASQ61K driver mutation, after either CRISPR-Cas9 CD133 knockout or Dox-inducible expression of CD133. CD133 knockout in BAKP cells increased trametinib-induced apoptosis by reducing anti-apoptotic BCL-xL, p-AKT, and p-BAD and increasing pro-apoptotic BAX. Conversely, Dox-induced CD133 expression diminished apoptosis in trametinib-treated cells, coincident with elevated pro-survival p-AKT, p-BAD, BCL-2, and BCL-xL and decreased activation of BAX and caspases-3 and -9. Inhibition of MEK with trametinib, in combination with pan-AKT inhibitor capivasertib (AZD5363) in BAKP cells with either CD133 overexpression or knockout in vitro reduced cell survival as measured by XTT, FACS analysis and colony formation assays. Further, in vivo studies with nude mice xenografted with Dox-inducible BAKP melanoma cells, showed significantly decreased tumor growth after xenografted mice were treated with trametinib alone or in combination with AZD5363. CD133 may therefore activate a survival pathway where (1) increased AKT phosphorylation and activation induces (2) BAD phosphorylation and inactivation, (3) decreases BAX activation, and (4) reduces caspases-3 and -9 activity and caspase-mediated PARP cleavage, leading to apoptosis suppression and drug resistance in melanoma. Targeting nodes of the AKT and MAPK survival pathways with both trametinib and AZD5363 highlights the potential for combination therapies for NRAS-mutant melanoma stem cells for the development of more effective treatments for patients with high-risk melanoma. Citation Format: Ryyan Alobaidi, Nusrat Islam, Yanjun R. Zhang, Mathew M. Shamo, Samuel Allsup, Cynthia M. Simbulan-Rosenthal, Dean S. Rosenthal. Inhibition of both MAPK and AKT pathways overcomes resistance of NRAS-mutant melanoma stem cells to apoptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6142.
Abstract 6046: Enhanced <i>Acod1</i> expression in cancer cells promotes immune evasion
Authors: James H. Schofield, Joseph Longo, Sean Murphy, Ryan Sheldon, Mark A. Hawk, Emma Albano, Russell G. Jones, Xin Lu, Zachary T. Schafer
Journal: Cancer Research (2023)

Abstract The monoclonal antibody αPD-1 used in immune checkpoint blockade (ICB) therapy has made a substantial impact in clinical outcomes for melanoma, lung, and breast cancer patients. Despite the success of ICB in these contexts, such strategies are not universally effective due to unresponsiveness or development of resistance by the malignant cells. Poor understanding of the molecular mechanisms leading to ICB resistance is a crucial barrier to more effective ICB. Recent studies have demonstrated that the metabolic milieu of the tumor microenvironment (TME) can modulate the anti-tumor immune response. However, the specific mechanisms by which the secretion of cancer cell metabolites into the TME impacts the efficacy of ICB in unresponsive tumors remains poorly understood. To better characterize the factors that influence ICB, we utilized a murine model (Smad4−/−/Pten−/−/Trp53−/−) of castration-resistant prostate cancer (CRPC) that is responsive to αPD-1. Serial culture and passage of residual tumor cells following exposure to αPD-1 treatment into new recipient mice allowed us to develop an ICB-insensitive CRPC cell line. Unbiased metabolic analysis revealed that the αPD-1 resistant cells produced elevated levels of itaconate, a metabolite whose biological functions in epithelial cells remain poorly characterized. Consistent with this finding, the resistant cells display increased expression of aconitate decarboxylase 1 (Acod1), the enzyme responsible for itaconate production. Additionally, we have identified established human epithelial cancer cell lines which express high levels of ACOD1. Interestingly, conditioned media (CM) from the Acod1-high cell lines, but not the Acod1-low lines, restricts the proliferation and activation of naïve CD8+ T cells in vitro. CRISPR-mediated Acod1 reduction in the αPD-1 insensitive cells (Acod1KO) produces CM which promotes increased naïve CD8+ T proliferation and activation, suggesting a link between Acod1 abundance in cancer cells and the activity of cytotoxic T cells. Furthermore, Acod1KO tumors have increased CD8+ tumor infiltrating lymphocytes (TILs) and increased sensitivity towards αPD-1 ICB in vivo. Taken together, these data suggest that cancer cell intrinsic ACOD1 abundance may be predictive of ICB efficacy. Citation Format: James H. Schofield, Joseph Longo, Sean Murphy, Ryan Sheldon, Mark A. Hawk, Emma Albano, Russell G. Jones, Xin Lu, Zachary T. Schafer. Enhanced Acod1 expression in cancer cells promotes immune evasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6046.
Abstract 4044: Development of UCT-01-097, a novel orally available ERK1/2 inhibitor for the treatment of ERK1/2 dependent cancers
Authors: Neil A. O'Brien, Martina S. McDermott, Brendan M. O'Boyle, Corey M. Reeves, Michael Bartberger, Oliver Loson, Kevin Chau, Jenny J. Hong, Weiping Jia, Naeimeh Kamranpour, Tong Luo, Raul Ayala, Athena M. Madrid, John A. Glaspy, Brian M. Stoltz, Dennis J. Slamon
Journal: Cancer Research (2023)

Abstract The MAPK signaling pathway is the most commonly mutated and/or dysregulated pathway in cancer. Strategies to target it have yielded some success with inhibitors against KRASG12C and BRAF, and to a lesser extent, MEK1/2. However, the impact of these molecules is often limited by toxicity and rapid and diverse mechanisms of resistance; both adaptive and/or acquired. For example, treatment with MAPK pathway targeting agents results in compensatory activation of the downstream mediator ERK1/2 and enables tumors to subvert the targeted therapy. Thus, targeting ERK1/2 provides promising potential advantages in overcoming and/or preventing adaptive and acquired resistance. We evaluated multiple preclinical and clinically staged ERK1/2 inhibitors—including ERAS-007 and BVD-523—in a 500+ cell line screening platform and identified cancers with subpopulations that are sensitive to this class of inhibitor. KiNativ analyses helped to inform the differences in sensitivity/selectivity that we observed between each ERK1/2 inhibitor. Comprehensive molecular profiling of the cell lines at baseline allowed us to screen for potential molecular markers of sensitivity/resistance to these compounds. Using this platform, we have developed a novel, potent ERK1/2 small molecule inhibitor, UCT-01-097, with improved selectivity over other clinically staged inhibitors. These data, coupled with the broad spectrum of in vitro responses, suggests an improved therapeutic index with this molecule. UCT-01-097 shows kinase selectivity in both cell free and in-cell assays and robust efficacy in panel of pancreatic PDX models. Inhibition of xenograft tumor growth was achieved using both daily dosing and intermittent dosing schedules. We have successfully submitted a regulatory IND and are currently enrolling a Phase 1 clinical trial in advanced solid tumors for treatment with UCT-01-097 (NCT04761601). Citation Format: Neil A. O'Brien, Martina S. McDermott, Brendan M. O'Boyle, Corey M. Reeves, Michael Bartberger, Oliver Loson, Kevin Chau, Jenny J. Hong, Weiping Jia, Naeimeh Kamranpour, Tong Luo, Raul Ayala, Athena M. Madrid, John A. Glaspy, Brian M. Stoltz, Dennis J. Slamon. Development of UCT-01-097, a novel orally available ERK1/2 inhibitor for the treatment of ERK1/2 dependent cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4044.
Abstract 6039: ELOVL5 affects prostate cancer cell proliferation and modulates the AR pathway
Authors: Silvia D. Rodrigues, Caroline Ribeiro, Isadora Teixeira, Hubert Pakula, Giuseppe N. Fanelli, Fabio Socciarelli, Lisa Butler, Johannes Swinnen, Massimo Loda
Journal: Cancer Research (2023)

Abstract Prostate cancer (PCa) is characterized by alterations in lipid metabolism, exemplified by increased rates of de novo lipogenesis and elongation by fatty acid elongase enzymes known as ELOVLs (elongation of very long chain fatty acids). We have previously shown that the ELOVL family members ELOVL2, 5, and 7 are Androgen Receptor (AR)-regulated proteins; and that ELOVL5 is overexpressed in both primary and castration-resistant prostate cancer. To confirm the role of ELOVL5 activity in prostate carcinogenesis, we generated genetically engineered mouse models (GEMM) with deletion of Elovl5, validated by immunohistochemistry, in combination with the overexpression of c-Myc, an oncogene known to affect lipid metabolism in cancer cells. As expected, we observed alterations in the lipid profile of the murine prostate with the partial deletion of Elovl5, as determined by a significant reduction in levels of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) with long-chain fatty acids (22 carbons) and increased levels of PE with short-chain fatty acids (14 carbons), suggesting an overall shortening on acyl chains of the most common phospholipid species. Interestingly, we also observed that the heterozygous deletion of Elovl5 reduced the expression levels of the AR on the anterior lobe of the murine prostate, in comparison to tissue from Elovl5 wild type mice. Preliminary data also indicates a modulation in prostate volume when Elovl5 is genetically deleted in comparison to tissue from wild type mice. Heterozygous Elovl5 deletion did not affect healthy tissue.To explore biological effects, we generated a 3D organoid line derived from the prostate of mice with homozygous deletion of Elovl5 and overexpression of c-Myc. We found that Elovl5 knock-out decreased organoid diameter and proliferation of c-Myc-driven cells compared to Elovl5 WT. This effect was potentiated when organoids were treated with Enzalutamide, suggesting that targeting Elovl5 may sensitize prostate cells to anti-androgen therapy.Our findings suggest lipid elongation via ELOVL5 as a potential therapeutic target for PCa. Citation Format: Silvia D. Rodrigues, Caroline Ribeiro, Isadora Teixeira, Hubert Pakula, Giuseppe N. Fanelli, Fabio Socciarelli, Lisa Butler, Johannes Swinnen, Massimo Loda. ELOVL5 affects prostate cancer cell proliferation and modulates the AR pathway. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6039.
Abstract 6044: Identification and molecular characterization of cancer cells survived under glucose starvation
Authors: Elimelech Nesher, Bar Levi, Hadas Levy, Raichel Cohen-Harazi, Igor Koman
Journal: Cancer Research (2023)

Abstract Tumors are heterogeneous, consisting of different cell subpopulations to allow tumor survival in variable conditions. We observed the survival of a small percentage of HCT116 cells under glucose starvation. We hypothesized that these cells represent a previously undescribed subpopulation able to adjust their metabolism in the absence of glucose. Here we aimed to characterize the metabolic and molecular properties allowing these cells to survive. We propagated individual clones from HCT116 cells and further analyzed a single clone descendants were able to survive glucose starvation. Biochemical and molecular analyses were performed under standard glucose conditions, under glucose starvation during adaptation period, and under glucose starvation after resumption of proliferation. Metabolic analysis by Seahorse revealed that surviving cells completely shifted their metabolism from glycolysis to oxidative phosphorylation. LC-MS metabolomics analysis revealed that during senescence-like adaptation the cells accumulate metabolites required for NAD synthesis. FAD, a co-factor involved in the TCA cycle, was not found in the dormant cells, while higher levels of carnosine, essential for ROS elimination, were observed. The metabolic shift toward enhanced oxidative phosphorylation was accompanied by increased production of ROS leading to DNA damage, reflected in an upregulation of the genes NUPR, ST6GAL1, and EGRF as observed by RNAseq. Cells that resumed proliferation were also characterized by enhanced expression of DNA damage repair genes and upregulated subunits of ATP-synthase, a key enzyme in oxidative phosphorylation. We suggest that cells predisposed to effective DNA repair have more time and capabilities to adjust their metabolism and to survive. Citation Format: Elimelech Nesher, Bar Levi, Hadas Levy, Raichel Cohen-Harazi, Igor Koman. Identification and molecular characterization of cancer cells survived under glucose starvation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6044.
Abstract 3023: Identifying colorectal cancer biomarkers using a targeted proteomics platform with extensive coverage
Authors: Justin Harbs, Matilda Rentoft, Xijia Liu, Beatrice S. Melin, Sophia Harlid, Bethany Van Guelpen
Journal: Cancer Research (2023)

Abstract Despite advances in treatment, colorectal cancer remains one of the leading causes of cancer-specific death. To decrease colorectal cancer mortality, better and more cost-efficient tools for risk prediction and early detection are needed. One area that has shown promise is using protein biomarkers, measured in blood, to detect individuals with early-stage disease or at increased risk. The primary aim of this study was therefore to identify novel protein biomarkers associated with colorectal cancer risk and the secondary aim was to validate protein biomarkers that had been described in previous studies. We included data and samples from 185 incident colorectal cancer cases and 185 controls (matched on age, sex, sampling date, and the number of freeze-thaw cycles) from the Northern Sweden Health and Disease Study (NSHDS). Samples were collected between six years and three months prior to the diagnosis date of each case and concentrations of 1536 individual proteins were measured in plasma samples using the Olink Explore 1536 platform (Olink Proteomics). Prior to statistical analyses, 249 proteins were excluded, either due to not passing quality control or having more than 50% of the concentrations below the limit of detection. In addition, we also excluded extreme outliers. Conditional logistic regression was used to estimate Odds Ratios (ORs) and 95% confidence intervals (95% CI) for the association between protein concentrations and colorectal cancer risk. Multivariable models were adjusted for predetermined colorectal cancer risk factors, including body mass index, alcohol consumption, physical activity, smoking status, and level of education. When considering p&amp;lt;0.005 as a cut-off, we identified 20 proteins that were associated with colorectal cancer risk. Our top hit was TFF3 (Trefoil Factor 3) which was positively associated with colorectal cancer at a high significance level (multivariable OR per SD: 1.84 95% CI: 1.38 - 2.45). TFF3 was significant in men (FDR&amp;lt;0.1), but not in women (pheterogeneity &amp;lt;0.05). In addition, several of the top 20 proteins such as AREG, MMP7, and CXCL16 have been linked to the diagnosis or prognosis of colorectal cancer in earlier studies. To conclude, we identified one novel protein biomarker, TFF3, strongly associated with colorectal cancer risk and validated several proteins previously linked to the diagnosis or prognosis of colorectal cancer. Citation Format: Justin Harbs, Matilda Rentoft, Xijia Liu, Beatrice S. Melin, Sophia Harlid, Bethany Van Guelpen. Identifying colorectal cancer biomarkers using a targeted proteomics platform with extensive coverage [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3023.